Immunohistochemical evaluation of urokinase plasminogen activator receptor in noninvasive and early invasive urothelial papillary neoplasia

OBJECTIVE: To investigate urokinase plasminogen activator receptor (uPAR) expression in urothelial papilloma and in noninvasive and early invasive papillary carcinoma. STUDY DESIGN: The study included 40 cases of papillary neoplasia of the urinary bladder subdivided into 10 cases of urothelial papilloma (UP); 10 of papillary carcinoma, grade 1; 10, grade 2 (G2); and 10, grade 3 (G3). Invasion of the subepithelial connective tissue was present in 5 cases of G2 and 7 cases of G3. According to the 2002 revision of the TNM system, these cases were defined as T1 and the others as Ta. uPAR expression was evaluated with an immunohistochemical technique in 5-microns-thick tissue sections. RESULTS: Difference in the distribution of positive cases in the 4 groups were statistically significant and greatest in G3. Statistically significant differences were also observed between Ta and T1 cases in terms of uPAR intensity. CONCLUSION: Detection of immunoreactivity for uPAR was associated with high grade UP carcinomas. These data indicate that uPAR is potentially an important prognostic factor in bladder carcinoma.     

POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix

Protein disorder is characterized by a lack of a stable 3D structure, and is considered to be involved in a number of important protein functions such as regulatory and signalling events. We developed a web application, the POODLE-S, which predicts the disordered region from amino acid sequences by using physicochemical features and reduced amino acid set of a position-specific scoring matrix. Availability: POODLE-S is available from http://mbs.cbrc.jp/poodle/poodle-s.html and can be used by both academic and commercial users.     

Exploiting a reduced set of weighted average features to improve prediction of DNA-binding residues from 3D structures

Predicting DNA-binding residues from a protein three-dimensional structure is a key task of computational structural proteomics. In the present study, based on machine learning technology, we aim to explore a reduced set of weighted average features for improving prediction of DNA-binding residues on protein surfaces. Via constructing the spatial environment around a DNA-binding residue, a novel weighting factor is first proposed to quantify the distance-dependent contribution of each neighboring residue in determining the location of a binding residue. Then, a weighted average scheme is introduced to represent the surface patch of the considering residue. Finally, the classifier is trained on the reduced set of these weighted average features, consisting of evolutionary profile, interface propensity, betweenness centrality and solvent surface area of side chain. Experimental results on 5-fold cross validation and independent tests indicate that the new feature set are effective to describe DNA-binding residues and our approach has significantly better performance than two previous methods. Furthermore, a brief case study suggests that the weighted average features are powerful for identifying DNA-binding residues and are promising for further study of protein structure-function relationship. The source code and datasets are available upon request.     

Prognostic value of morphometry in low grade papillary urothelial bladder neoplasms

OBJECTIVE: To analyze the prognostic value of morphometry in low grade papillary urothelial bladder neoplasms (LGPUBNs). STUDY DESIGN: The primary (most common) and secondary (second most common) histologic grades were considered in accordance with the 1998 World Health Organization/International Society of Urological Pathology and the 1999 World Health Organization classifications. With the primary grade, 54 cases were papillary urothelial neoplasms of low malignant potential (PUNLMPs) and 66 low grade papillary urothelial carcinomas (LGPUCs), whereas the secondary grade consisted of 45 PUNLMPs and 75 LGPUCs. To assess the proliferative index, an immunohistochemical study was performed. Regarding nuclear morphometry, an image analysis system on Feulgen-stained sections was utilized in different tumor zones (Zs): Z 1, 100-150 cells from the outer layers of the papillae; Z 2, 100-150 cells from the inner layers; and Z 3, 10 largest nuclei. In univariate studies, a t test, and Mann-Whitney U test and Kaplan-Meier curves were applied, whereas a Cox regression model was used for multivariate study of the variables: size, multiplicity, maximum Ki-67 index, mean nuclear area (MNA) and SD, mean nuclear perimeter and SD, and roundness factor. RESULTS: All 120 cases were followed for a mean of 76.6 months (range, 36-168). In univariate studies, many variables showed a significant correlation (p < 0.05) with recurrence prediction, relapse-free interval and histologic grade regardless of adjuvant therapy. Otherwise, only the MNA of the 10 largest nuclei (threshold, 52 microm2) and the maximum proliferative index (threshold, 7.9%) appeared as independent prognostic markers in the multivariate study. CONCLUSION: In LGPUBNs, the independent prognostic value of MNA of the 10 largest nuclei as well as the maximum proliferative index indicates the importance of histologic grade assessment based on the secondary (second most common) grade.     

Histometric features for the grading of prostatic carcinoma

Histometric features for the objective grading of prostatic adenocarcinoma in histologic specimens were analyzed in five cases each of well, moderately and poorly differentiated lesions. Tissue sections from the selected cases were stained by the Feulgen method and digitized by a video-based microphotometer. Twenty total fields were recorded for each grade: ten at high resolution (an image sampling of 0.5 micron per pixel) and ten at low resolution (0.8 micron per pixel), with two fields per case recorded at each resolution. The images were segmented by an automated expert system-guided scene segmentation procedure. The performance of that procedure was measured by comparing the automated counts of nuclei in the segmented fields to the visual counts made by a pathologist in the same fields. For well, moderately and poorly differentiated cases, respectively, the nuclear counts made by the expert system at high resolution were 2.7%, 4.2% and 4.7% higher than the visual counts (as estimated from a total of 6,628 nuclei), but 1.2%, 2.5% and 1.1% lower at low resolution (10,329 nuclei). High-resolution features and tissue textural features were computed for each case. The high-resolution features showed good separation between the three groups of cases. The tissue textural features showed consistent separation between well and moderately differentiated cases. The relaxation of the spatial resolution (to 0.8 micron/pixel spacing) did not affect the selection of features, but led to less separation between the data from different grades. In conclusion, the automated system performed satisfactorily in distinguishing sections of prostatic tumors of varying degrees of differentiation.     

Cytologic features of endometrial papillary serous carcinoma

Endometrial papillary serous carcinoma (EPSC) is an uncommon variant of endometrial carcinoma that histologically resembles ovarian serous carcinoma and has an aggressive clinical course. The cytomorphologic features of 17 patients with histologically confirmed EPSC of the endometrium were reviewed and compared with those of 20 patients with histologically typical endometrial adenocarcinoma (TEC). Preoperative cervicovaginal Papanicolaou smear results were available from 14 of the 17 patients with EPSC; 10 (71%) were positive, 1 (7%) was suspicious and 3 (21%) were negative for malignancy. Initial cervicovaginal smear results were available from all 20 patients with TEC; 7 (35%) were positive, 4 (20%) were atypical or suspicious and 9 (45%) were negative for malignancy. Twelve patients with EPSC had peritoneal washings or fluids examined; seven were positive and five negative. Twelve patients with TEC had peritoneal washings or fluids examined; two (17%) were positive and ten (83%) were negative. The cervicovaginal smears from patients with EPSC revealed numerous large tumor cells (with prominent nucleoli) frequently arranged in papillary clusters with background necrosis and, in two cases, amorphous material suggestive of psammoma bodies. In contrast, the smears of patients with TEC showed small to medium-sized cells with extensive phagocytosis and many background histiocytes. The diagnosis of EPSC should be considered when the cervicovaginal smear contains numerous papillary groups of large tumor cells with macronucleoli but without prominent phagocytosis, especially when structures suggestive of psammoma bodies are present. The peritoneal fluids in these patients are more often positive than in patients with TEC, a finding consistent with the propensity of EPSC to involve peritoneal surfaces.     

Observer variation in histopathological diagnosis and grading of cervical intraepithelial neoplasia.

To assess the variability among histopathologists in diagnosing and grading cervical intraepithelial neoplasia eight experienced histopathologists based at different hospitals examined the same set of 100 consecutive colposcopic cervical biopsy specimens and assigned them into one of six diagnostic categories. These were normal squamous epithelium, non-neoplastic squamous proliferations, cervical intraepithelial neoplasia grades I, II, and III, and other. The histopathologists were given currently accepted criteria for diagnosing and grading cervical intraepithelial neoplasia and asked to mark their degree of confidence about their decision on a visual linear analogue scale provided. The degree of agreement between the histopathologists was characterised by kappa statistics, which showed an overall poor agreement (unweighted kappa 0.358). Agreement between observers was excellent for invasive lesions, moderately good for cervical intraepithelial neoplasia grade III, and poor for cervical intraepithelial neoplasia grades I and II (unweighted kappa 0.832, 0.496, 0.172, and 0.175, respectively); the kappa value for all grades of cervical intraepithelial neoplasia taken together was 0.660. The most important source of disagreement lay in the distinction of reactive squamous proliferations from cervical intraepithelial neoplasia grade I. The histopathologists were confident in diagnosing cervical intraepithelial neoplasia grade III and invasive carcinoma (other) but not as confident in diagnosing cervical intraepithelial neoplasia grades I and II and glandular atypia (other). Experienced histopathologists show considerable interobserver variability in grading cervical intraepithelial neoplasia and more importantly in distinguishing between reactive squamous proliferations and cervical intraepithelial neoplasia grade I. It is suggested that the three grade division of cervical intraepithelial neoplasia should be abandoned and a borderline category introduced that entails follow up without treatment.     

Tissue architectural features for the grading of prostatic carcinoma

In research for the development of a computer-aided workstation for the objective grading of prostatic carcinoma, tissue architectural (histometric) features were analyzed in ten cases each of well-differentiated, moderately differentiated and poorly differentiated carcinoma (as subjectively graded by the consensus of a panel of experts). Sections were cut at 4 microns, stained by the Feulgen reaction and digitized by two different video-based photometric systems. Some images were interactively segmented, considering the histometric clues to be studied; others were automatically segmented by an expert system-guided technique. The latter procedure produced good results, with over 90% of the nuclei judged to be correctly segmented in 64% of the fields studied and over 80% in another 24% of the fields. While the number of nuclei per field provided some separation of well-differentiated from other lesions, the number of nuclei per gland distinguished between well-differentiated and moderately differentiated lesions. Simplicial decomposition of the images also provided a measure of the degree of differentiation, as did the "texture" of the nuclear placement, based on two run-length statistics. Combination of the run-length features distinguished the three categories of lesions with statistical significance. The results of this study provided insights into the problems (such as the effect of field boundaries) faced in the design of an computer-aided grading system. They also showed the value of expert system-guided scene segmentation and of such histometric features as the field cellularity and the number of nuclei per gland for the discrimination between lesions of different grades of differentiation.     

Architectural, morphometric and photometric features and their relationship to the main subjective diagnostic clues in the grading of prostatic cancer

Novel software was developed to perform quantitative measurements of architectural and nuclear features in tissue sections. A pilot study was then undertaken to determine the diagnostic relevance of these quantitative features in prostatic tissue and the relationship of these objective features to the subjective clues used by practicing pathologists in the grading of prostatic adenocarcinoma. From a group of 82 cases of adenocarcinoma of the prostate with long-term follow-up, a subset of 15 cases that included 5 each in Mostofi grades I, II and III was carefully selected for analysis. Consecutive sections from each case were stained with hematoxylin and eosin or the Feulgen stain for visual and cytometric evaluations, respectively. The most important differences in the objective architectural features observed between the Mostofi grade I and II cases were the number of nuclei per gland and their distance from the glandular center. Significant differences were also noted in gland size and the variation in gland size. The Mostofi grades were also significantly different in terms of quantitative high-resolution features measuring nuclear size and its variation, total nuclear DNA content and the proportion of very aneuploid nuclei. There was a fairly good agreement between many of the subjective diagnostic clues and their corresponding quantitative architectural and nuclear features. This work (1) significantly extended the capabilities of our PC-based microphotometer system to analyze glandular tissue specimens, (2) provided insight into the objective bases for the expert diagnosis of adenocarcinomas of the prostate and (3) gave preliminary evidence of the ability of quantitative architectural features and high-resolution cytometric features to discriminate between the major diagnostic categories of these lesions.     

Computer-based malignancy grading of astrocytomas employing a support vector machine classifier, the WHO grading system and the regular hematoxylin-eosin diagnostic staining procedure

OBJECTIVE: To investigate and develop an automated technique for astrocytoma malignancy grading compatible with the clinical routine. STUDY DESIGN: One hundred forty biopsies of astrocytomas were collected from 2 hospitals. The degree of tumor malignancy was defined as low or high according to the World Health Organization grading system. From each biopsy, images were digitized and segmented to isolate nuclei from background tissue. Morphologic and textural nuclear features were quantified to encode tumor malignancy. Each case was represented by a 40-dimensional feature vector. An exhaustive search procedure in feature space was utilized to determine the best feature combination that resulted in the smallest classification error. Low and high grade tumors were discriminated using support vector machines (SVMs). To evaluate the system performance, all available data were split randomly into training and test sets. RESULTS: The best vector combination consisted of 3 textural and 2 morphologic features. Low and high grade cases were discriminated with an accuracy of 90.7% and 88.9%, respectively, using an SVM classifier with polynomial kernel of degree 2. CONCLUSION: The proposed methodology was based on standards that are common in daily clinical practice and might be used in parallel with conventional grading as a second-opinion tool to reduce subjectivity in the classification of astrocytomas.     

Cytologic features of urothelial carcinoma in catheterized urine with cellular fragments

OBJECTIVE: To identify architectural and cytomorphologic differences that might help distinguish urothelial neoplasms from instrumentation artifact. STUDY DESIGN: We examined 73 cytologic smears of catheterized urine containing urothelial cell clusters between 1998 and 2004. All patients had at least 1 follow-up biopsy. Smears were reviewed for several morphologic features blindly, without knowledge of the follow-up diagnosis. RESULTS: Of the 73 smears, 39 had a benign diagnosis on follow-up biopsy, and 34 had urothelial carcinoma. Cytoplasmic collar, regular and rounded fragment borders, and fine nuclear chromatin were statistically more common in benign smears than those with urothelial carcinoma (p < 0.0001). No significant differences were identified with regard to the presence of background inflammation or nucleoli in the urine specimens. Of the 17 smears that had a cytoplasmic collar, regular fragment borders and fine nuclear chromatin, only 1 (6%) was found to have urothelial carcinoma on follow-up biopsy. All 20 smears in which all 3 features were absent were proven malignant on biopsy. CONCLUSION: Certain architectural and nuclear features can help differentiate urothelial neoplasms from instrumentation artifact in urine cytologic smears.     

Value of quantitative cytologic studies in the grading of papillary tumors of human urinary bladder

Mitotic indices and nuclear volumes were determined in 10 papillomas, 20 grade I, 20 grade II and 20 grade III papillary carcinomas of the urinary bladder. The mean mitotic indices were 1.22% in papillomas, 2.77% in grade I carcinomas, 8.2% in grade II carcinomas and 15.25% in grade III carcinomas. The nuclear volumes showed a gradual shift to larger values paralleling the histological degree. It is suggested that these objective parameters might be especially useful for the cytological assessment of exfoliated tumor cells.     

Clinical and cytologic features of papillary neoplasms of the breast

OBJECTIVE: To compare the cytologic features benign and malignant papillary breast lesions. STUDY DESIGN: We reviewed the clinical and cytologic features in 29 cases of intraductal papilloma and 26 cases of atypical papilloma or papillary carcinoma that had been diagnosed by histologic examination. The diameter of the mass was examined as a clinical feature. The cytologic features evaluated were as follows: bloody background, row of tall columnar cells, naked bipolar nuclei, hemosiderin-laden macrophages, myoepithelial cells, single scattered atypical cells, cellularity, nuclear atypia, nuclear grade, apocrine metaplasia, eosinophilic cytoplasmic granules, papillary clusters, small papillae, cell balls and large sheets. RESULTS: Of the features evaluated, the diameter of the mass, naked bipolar nuclei and cell balls differed significantly between benign and atypical or malignant papillary neoplasms. The average diameter of a benign papillary neoplasm was 1.8 cm, and that of an atypical or malignant papillary neoplasm was 2.2 cm (p = 0.042). Naked bipolar nuclei were found in 27 cases of benign papillary neoplasm (93.1%) versus 19 cases of atypical or malignant papillary neoplasm (73.1%) (p = 0.050). Cell balls were found in 14 (48.3%) and 21 (80.8%) cases, respectively (p = 0.012). All 6 cases in which cell balls were present and naked bipolar nuclei were absent proved to be atypical or malignant papillary neoplasms. Of 17 cases in which cell balls were absent and naked bipolar nuclei present, 13 (76.5%) were benign papillary neoplasms. CONCLUSION: Most cytologic features overlapped in benign and atypical or malignant papillary neoplasms. Although they were not pathognomonic, naked bipolar nuclei and cell balls were cytologic features that differed significantly between benign and atypical or malignant papillary neoplasms. When papillary neoplasms of the breast are suspected in a cytologic smear, the combination of clinical examination, mammography and cytologic features should be considered to make the correct diagnosis.     

Improvement of biohydrogen production using a reduced pressure fermentation

Bioprocess and Biosystems Engineering - This study investigated the effect of reduced pressure on biohydrogen production in an upflow anaerobic sludge blanket (UASB) reactor from whey permeate. The...     

Cytologic features of cribriform-morular variant of papillary carcinoma of the thyroid: a case report

BACKGROUND: While the histology of cribriform-morular variant of papillary thyroid carcinoma has been well documented, its appearance on cytologic smears has rarely been described given the rarity of this tumor. CASE: A 28-year-old woman had a neck lump for an unspecified duration for which she sought medical attention. She was previously well, and there was no significant family history of illness. Fine needle aspiration of the thyroid mass disclosed columnar cells with fine to granular chromatin and nucleargrooves associated with papillary fragments and acinar formation. Occasional groups of epithelial cells forming morules, previously unreported on cytology, were present. An excision specimen of the left thyroid nodule revealed morphologic features of cribriform-morular variant of papillary carcinoma of the thyroid. CONCLUSION: A diagnosis of cribriform-morular variant of papillary carcinoma of the thyroid could be established on fine needle aspiration cytology, prompting exclusion of familial adenomatous polyposis and distinguishing it from other, more aggressive variants of thyroid carcinoma, such as columnar cell carcinoma.     

Unipolar brush cells develop a set of characteristic features in primary cerebellar cultures

Brain Cell Biology - The unipolar brush cells (UBCs) are a class of excitatory interneurons recently discovered in the cerebellar granular layer. UBCs differ morphologically and biochemically from...